--junk_reads [int] This percentage of reads will be low-complexity junk (default: 0) [more info](https://github.com/rrwick/Badread#junk-and-random-reads)
--random_reads [int] This percentage of reads will be random sequence (default: 0) [more info](https://github.com/rrwick/Badread#junk-and-random-reads)
--chimeras [int] Percentage at which separate fragments join together (default: 0) [more info](https://github.com/rrwick/Badread#chimeras)
--start_adapter_seq [str] Adapter sequence for read starts (default: '')
--end_adapter_seq [str] Adapter sequence for read ends (default: '')
General:
--seed [int] Random number generator seed for deterministic output (default: different ouput each time)
The only parameter needed is one of these: `--all_gapcloser`, `--GM_gapcloser`, `--LR_gapcloser` or `--TGS_gapcloser`. It specifies the gapcloser tool(s) to run. This will generate a random sequence and corresponding random reads.
If you want the pipeline to take as input your own sequence, use `--assembly` parameter. Your assembly must be a single fasta file without gaps. If you have a multi fasta file, split it and run the pipeline for each sequence.
If you want the pipeline to take as input your own reads, use `--reads` parameter. These reads can not be specified without the associated assembly. You must also give the coordinates of reads on your assembly in BED format with option `--reads_coord`.
## Output files
Output files are stored in the output directory specified by `--outdir` option (default: `./results`). It contains:
* `report.html`: An html report to show the efficiency of each gapcloser.
* `pipeline_trace.txt`: A table of each process run by Nextflow and some info such as mempry used, running time...
* `data/`: A directory with CSV files used to generate the report, assembly gapclosed by gapcloser, sequence and reads generated or given to the pipeline.
* `images/`: A directory with images of each gap and reads mapped on these regions. There is one directory of each gapcloser tool.
* `plots/`: A directory with plots generated for the report.
## Dependencies
If you do not use the singularity image, this is a list of required elements to install before running the workflow.